The Stags boss was upset on the day by seeing the assistant referee miss Jamie Murphy's shot come down off the bar and cross the line that should have had them 1-0 up and in the driving seat.
And he was doubly incensed after replays then showed him that Omari Patrick's winner was a yard offside.
“Those two decisions cost us three points in the game without a doubt,” said Clough, as his side slipped out the top seven.
“There was a mistake by the assistant when we'd scored a perfectly good goal which was well over the line.
“After that the same assistant failed to spot their lad offside for their goal. He was a yard offside.
“Elliott Hewitt stands up and you can clearly see it from the lines on the pitch. The assistant goes towards putting his flag up and then for some reason doesn't That is the game in a nutshell.
“We played well and created lots of chances. Yes, we were a little bit wasteful at times, but we were not wasteful on those two occasions.
“Our supporters have travelled seven or eight hours to be there and I just think they all deserve better.”Clough believes his side have had the rough end of the stick on decisions all season.
“We've had it for 40-0dd games,” he said.
“It started at Colchester in our third game of the season where we're in control and in the 93rd minute the referee inexplicably gave a penalty. It should have been three straight wins.
“Intermittently over the next 40 games we have had some very, very poor decisions go against us. Every club will say that they've had a a few.
“But I defy any club to say they've had as many as we've had go against us. Two offside goals at Tranmere - it goes on and on – a litany of mistakes that have been made, unfortunately, against us.
“I think as a club our supporters and players deserve better.”
In contrast, promotion rivals Port Vale have had it go for them recently.
Clough said: “The difference is makes was underlined recently when Port Vale were at home to Oldham about 10 days ago and one of their best players made a tackle which was a red card all day about yards in front of the referee, who has an unimpeded view, and he gave him a yellow card.
“You compare that with George Lapslie's red card and it's incredible. So they should be missing that player and might not have won the game.
“Oldham are fighting relegation and ended up losing 3-2 when they should have been playing against 10 men and might have got something out of the game.
“It impacts their season massively as well.”
Clough believes his complaints over standards have gone nowhere.
“The head of the officials told me that when referees make a mistake they are stood down for a game or two to think about it,” he said.
“After the mistake against Port Vale that referee was not stood down. He has Exeter v Colchester a week later and ended up fourth official in a Championship game as a substitute last night – the biggest game in the Championship – Forest v West Brom.
“So when you've made a mistake of that magnitude, to get those two games is quite puzzling really.
“When Port Vale played at Hartlepool the handball which wasn't given in the penalty area, again from a referee unimpeded 10 yards away, is quite staggering as well.
“We have had the decisions go against us this season and the difference it makes is incredible.
“We were chasing Port Vale for automatic promotion prior to the two games and they get a couple of decisions go in their favour and we get a couple against us it makes a huge difference unfortunately.”